What are some things that most scientists once suspected to be true that most scientists today know to be false?

One famous example (I assume covered in your original text, though) is the http://en.wikipedia.org/wiki/Continental_drift#Rejection_of_Wegener.27s_theory.2C_and_subsequent_vindication, although there were reasonable bases for this. Pluto being a planet. I heh'ed, but it's important to note that nothing about Pluto itself is held to have changed, only the context in which it inhabits the solar system.

I'm most interested in things that were defended in their day and died a hard death because so many people wanted them to be true. Pluto being a planet.

There was a demon that lived in the air. They said whoever challenged him would die. Their controls would freeze up, their planes would buffet wildly, and they would disintegrate. The demon lived at Mach 1 on the meter, seven hundred and fifty miles an hour, where the air could no longer move out of the way. He lived behind a barrier through which they said no man could ever pass. They called it the sound barrier.-- http://www.imdb.com/title/tt0086197/quotes?qt=qt0377963

You might be interested in reading Kuhn's http://www.worldcat.org/oclc/93075 (please try to enjoy it despite the way that the word 'paradigm' has become a meaningless buzzword in the years since that book's popularity). As for specific examples, reading the history of any field of science will provide you with many of them.

Since Ray Bradbury has just died, it seems apropos to bring up one of the stories from The Illustrated Man: At one time, Venus was considered to be cloudy and rainy. Like Seattle, without coffee.

I've never read that book, but here are some off the top of my head.... Evolution through individuals (as opposed to populations) http://en.wikipedia.org/wiki/Lamarckism Miasmas, the spread of disease through "bad air", as opposed to treatable sources (as opposed to the germ theory of disease....poor Semmelweis...) http://en.wikipedia.org/wiki/Miasma_theory_of_disease

It's in the wiki link, but I love preformism, the theory that sperm has fully formed little people in them.

As a materials engineer, my favorite:http://www.glassnotes.com/WindowPanes.html

A lot of medical/biological stuff qualifies. People use to think that a child's sex was solely determined by the mother, unlike as we now know by the father; also, all failure to conceive children was the woman's fault (whether by her 'willfullness' in denying her husband his rightful heir or because she was 'barren'). And don't forget how they thought that the mother's prenatal experiences would affect her unborn child --- "she was scared by a big dog while she was pregnant, and that's why Little Johnny is terrified of all dogs." One that I've always thought hilarious, since I've had asthma all my life: people used to think smoking was good for asthmatics: if someone was having an asthma attack, you'd give them a cigarette or even better a cigar "to relax their throat and lungs." And up until the mid-1800s, it was actually considered foolish for a doctor to wash his hands or instruments --- indeed, the filthier a doctor's frock coat was when he went to deliver a baby, was merely considered proof of that doctor's experience.